Transcriptome analysis of liver, gill and intestine in rainbow trout (Oncorhynchus mykiss) symptomatically or asymptomatically infected with Vibrio anguillarum

Yang, Qian; Yang, Xiaodong; Liu, Meng-Qun; Zeng, Chu; Zhao, Hong-Kui; Xiang, Kai-Wen; Hou, Zhi-Shuai; Wen, Haishen; Li, Jifang

doi:10.1016/j.fsi.2023.108643

Cited by 3 publications

(1 citation statement)

References 72 publications

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“…In rainbow trout, most of the enriched pathways were involved in immune and inflammatory response of including the NF-κB signalling pathway. On the other hand, it was reported in turbot that, the protein interactions involved in TGF-β signalling pathway, the production of inflammatory factors, and endocytosis regulation were most significantly enriched [ 20 , 21 ]. In addition, immune gene expression studies after V. anguillarum challenge have been conducted in Japanese flounder ( Paralichthys olivaceus ).…”

Section: Discussionmentioning

confidence: 99%

Insights into the connection between pathogen water eDNA and disease progression in zebrafish infected with Vibrio anguillarum

Henard,

Blonç,

et al. 2024

Comparative Immunology Reports

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Section: Discussionmentioning

confidence: 99%

Insights into the connection between pathogen water eDNA and disease progression in zebrafish infected with Vibrio anguillarum

Henard,

Blonç,

et al. 2024

Comparative Immunology Reports

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Identification, characterization and complete genome analysis of a Vibrio anguillarum isolated from Sebastes schlegelii

Li,

Sun,

Tan

et al. 2024

Microbial Pathogenesis

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Epigenomics of embryogenesis in turbot (Scophthalmus maximus)

Aramburu,

Pardo,

Jimenez-Gonzalez

et al. 2024

Preprint

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Embryogenesis is the crucial first step of ontogeny, where an organism with a complex body plan arises from a single undifferentiated totipotent cell. This process is orchestrated by dynamic changes in transcriptional regulation, influenced by chromatin accessibility and nucleotide and histone modifications constituting epigenetic signals enabling access to transcription factors. The epigenomic regulation of embryogenesis has been studied in model fishes, but little attention has been paid to farmed fish - where traits of importance to aquaculture rely on early developmental processes. This study, framed within the AQUA-FAANG consortium, reports a comprehensive regulatory atlas of embryogenesis for turbot (Scophthalmus maximus), a farmed flatfish representing order Pleuronectiformes. 14,560 genes were expressed in the embryonic transcriptome with > 90% showing differential expression across consecutive stages. By integrating multi-histone ChIP-Seq marks with ATAC-Seq, we built a genome-wide chromatin state model, defining promoter and enhancer activity across stages. Transcription factor binding motif (TFBM) analysis of differentially active promoters and enhancers revealed dynamism in regulated gene functions, with more than half the TFBM enriched in a single developmental transition. Significant shifts in chromatin accessibility occurred across stages, most notably during the transition from shield to early segmentation, suggesting a profound chromatin reorganization underpins somitogenesis and early organ development. Most changes in chromatin accessibility across stages did not involve promoter regions of differentially expressed genes, suggesting a trend of promoter accessibility preceding gene transcriptional activity. Comparative analyses with zebrafish revealed a global transcriptomic correlation of single copy orthologs at matched stages of embryogenesis across species. While conserved expression dynamics were revealed for many orthologous Hox genes, notable cross-species differences were identified from before zygotic genome activation leading up to hatching. This multi-omics investigation provides a novel atlas of non-coding regulatory elements controlling turbot development, with key applications for flatfish biology and enhancing sustainable aquaculture.

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Transcriptome analysis of liver, gill and intestine in rainbow trout (Oncorhynchus mykiss) symptomatically or asymptomatically infected with Vibrio anguillarum

Cited by 3 publications

References 72 publications

Insights into the connection between pathogen water eDNA and disease progression in zebrafish infected with Vibrio anguillarum

Insights into the connection between pathogen water eDNA and disease progression in zebrafish infected with Vibrio anguillarum

Identification, characterization and complete genome analysis of a Vibrio anguillarum isolated from Sebastes schlegelii

Epigenomics of embryogenesis in turbot (Scophthalmus maximus)

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